Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States
Abstract
Rhodopseudomonas palustris is a purple nonsulfur anoxygenic phototrophic bacterium that is ubiquitous in soil and water. R. palustris is metabolically versatile with respect to energy generation and carbon and nitrogen metabolism. We have characterized and compared the baseline proteome of a R. palustris wild-type strain grown under six metabolic conditions. The methodology for proteome analysis involved protein fractionation by centrifugation, subsequent digestion with trypsin, and analysis of peptides by liquid chromatography coupled with tandem mass spectrometry. Using these methods, we identified 1664 proteins out of 4836 predicted proteins with conservative filtering constraints. A total of 107 novel hypothetical proteins and 218 conserved hypothetical proteins were detected. Qualitative analyses revealed over 311 proteins exhibiting marked differences between conditions, many of these being hypothetical or conserved hypothetical proteins showing strong correlations with different metabolic modes. For example, five proteins encoded by genes from a novel operon appeared only after anaerobic growth with no evidence of these proteins in extracts of aerobically grown cells. Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states.
- Authors:
- ORNL
- {Greg} B [ORNL
- University of British Columbia, Vancouver
- University of Washington, Seattle
- Ohio State University
- {Bob} L [ORNL
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 978060
- DOE Contract Number:
- DE-AC05-00OR22725
- Resource Type:
- Journal Article
- Resource Relation:
- Journal Name: Journal of Proteome Research; Journal Volume: 5; Journal Issue: 2
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; CARBON; CENTRIFUGATION; CHROMATOGRAPHY; DIGESTION; FRACTIONATION; GENES; MASS SPECTROSCOPY; METABOLISM; NITROGEN; NITROGEN FIXATION; PEPTIDES; PROTEINS; RHODOPSEUDOMONAS; SOILS; STRAINS; TRYPSIN; WATER
Citation Formats
Verberkmoes, Nathan C, Shah, Manesh B, Lankford, Patricia K, Pelletier, Dale A, Strader, Michael B, Tabb, Dave L, McDonald, W Hayes, Barton, John W, Hurst, Gregory, Hauser, Loren John, Davison, Brian H, Beatty, Thomas, Harwood, Caroline S, Tabita, F Robert, Hettich, Robert, and Larimer, Frank W. Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States. United States: N. p., 2006.
Web. doi:10.1021/pr0503230.
Verberkmoes, Nathan C, Shah, Manesh B, Lankford, Patricia K, Pelletier, Dale A, Strader, Michael B, Tabb, Dave L, McDonald, W Hayes, Barton, John W, Hurst, Gregory, Hauser, Loren John, Davison, Brian H, Beatty, Thomas, Harwood, Caroline S, Tabita, F Robert, Hettich, Robert, & Larimer, Frank W. Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States. United States. doi:10.1021/pr0503230.
Verberkmoes, Nathan C, Shah, Manesh B, Lankford, Patricia K, Pelletier, Dale A, Strader, Michael B, Tabb, Dave L, McDonald, W Hayes, Barton, John W, Hurst, Gregory, Hauser, Loren John, Davison, Brian H, Beatty, Thomas, Harwood, Caroline S, Tabita, F Robert, Hettich, Robert, and Larimer, Frank W. Sun .
"Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States". United States.
doi:10.1021/pr0503230.
@article{osti_978060,
title = {Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States},
author = {Verberkmoes, Nathan C and Shah, Manesh B and Lankford, Patricia K and Pelletier, Dale A and Strader, Michael B and Tabb, Dave L and McDonald, W Hayes and Barton, John W and Hurst, Gregory and Hauser, Loren John and Davison, Brian H and Beatty, Thomas and Harwood, Caroline S and Tabita, F Robert and Hettich, Robert and Larimer, Frank W},
abstractNote = {Rhodopseudomonas palustris is a purple nonsulfur anoxygenic phototrophic bacterium that is ubiquitous in soil and water. R. palustris is metabolically versatile with respect to energy generation and carbon and nitrogen metabolism. We have characterized and compared the baseline proteome of a R. palustris wild-type strain grown under six metabolic conditions. The methodology for proteome analysis involved protein fractionation by centrifugation, subsequent digestion with trypsin, and analysis of peptides by liquid chromatography coupled with tandem mass spectrometry. Using these methods, we identified 1664 proteins out of 4836 predicted proteins with conservative filtering constraints. A total of 107 novel hypothetical proteins and 218 conserved hypothetical proteins were detected. Qualitative analyses revealed over 311 proteins exhibiting marked differences between conditions, many of these being hypothetical or conserved hypothetical proteins showing strong correlations with different metabolic modes. For example, five proteins encoded by genes from a novel operon appeared only after anaerobic growth with no evidence of these proteins in extracts of aerobically grown cells. Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states.},
doi = {10.1021/pr0503230},
journal = {Journal of Proteome Research},
number = 2,
volume = 5,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
-
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris
Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustrismore » -
Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under photoheterotrophic growth conditions with reduced carbon sources
Rhodopseudomonas palustris is unique among characterized nonsulfur purple bacteria because of its capacity for anaerobic photoheterotrophic growth using aromatic acids. Like growth with other reduced electron donors, this growth typically requires the presence of bicarbonate/CO{sub 2} or some other added electron acceptor in the growth medium. Proteomic studies indicated that there was specific accumulation of form I ribulose 1, 5-bisphosphate carboxylase/oxygenase (RubisCO) subunit proteins (CbbL and CbbS), as well as the CbbX protein, in cells grown on benzoate without added bicarbonate; such cells used the small amounts of dissolved CO{sub 2} in the medium to support growth. These proteins weremore » -
Preservation of H 2 production activity in nanoporous latex coatings of Rhodopseudomonas palustris CGA009 during dry storage at ambient temperatures: Preservation of R. palustris latex coatings
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Uptake of benzoate by Rhodopseudomonas palustris grown anaerobically in light
The uptake and anaerobic metabolism of benzoate were studied in short-term experiments with phototrophic cells of Rhodopseudomonas palustris. Cells that were preincubated and assayed anaerobically in the presence of 1 mM dithiothreitol accumulated (7-/sup 14/C)benzoate at a rate of at least 0.5 nmol x min/sup -1/ x mg/sup -1/ of protein. Cells that were preincubated aerobically, or anaerobically in the absence of a reducing agent or an electron donor such as succinate, took up benzoate at reduced rates. Benzoate was removed from the external medium with remarkably high efficiency; initial uptake rates were independent of substrate concentration, and uptake remainedmore »